Ancestors               tree utility function
Laurasiatherian         Laurasiatherian data (AWCMEE)
NJ                      Neighbor-Joining
SH.test                 Shimodaira-Hasegawa Test
allTrees                Compute all trees topologies.
ancestral.pml           Ancestral character reconstruction.
as.splits               Splits representation of graphs and trees.
bab                     Branch and bound for finding all most
                        parsimonious trees
bootstrap.pml           Bootstrap
chloroplast             Chloroplast alignment
consensusNet            Computes a 'networx' object from a collection
                        of splits.
designTree              Compute a design matrix or non-negative LS
dfactorial              Arithmetic Operators
dist.hamming            Pairwise Distances from Sequences
distanceHadamard        Distance Hadamard
getClans                Clans, slices and clips
hadamard                Hadamard Matrices and Fast Hadamard
                        Multiplication
lento                   Lento plot
midpoint                Tree manipulation
modelTest               ModelTest
nni                     Tree rearrangements.
parsimony               Parsimony tree.
phangorn-package        Phylogenetic analysis in R
phyDat                  Conversion among Sequence Formats
plot.networx            Plot phylogenetic networks
pml                     Likelihood of a tree.
pmlCluster              Stochastic Partitioning
pmlMix                  Phylogenetic mixture model
pmlPart                 Partition model.
read.aa                 Read Amino Acid Sequences in a File
simSeq                  Simulate sequences.
splitsNetwork           Phylogenetic Network
treedist                Distances between trees
upgma                   UPGMA and WPGMA
yeast                   Yeast alignment (Rokas et al.)
